X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=d74cd31cac5e43132590b4889f192babedef1d83;hb=4b7d3640209c4434d569c746672cf9eed4250ace;hp=1785d4af7746aeff3751e5f6aee63d802e912f04;hpb=3740241b6d0dfa109dc81847afe58f17497c39e8;p=jalview.git diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java index 1785d4a..d74cd31 100644 --- a/test/jalview/project/Jalview2xmlTests.java +++ b/test/jalview/project/Jalview2xmlTests.java @@ -23,20 +23,47 @@ package jalview.project; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertFalse; import static org.testng.Assert.assertNotNull; +import static org.testng.Assert.assertNotSame; import static org.testng.Assert.assertNull; import static org.testng.Assert.assertSame; import static org.testng.Assert.assertTrue; +import java.awt.Color; +import java.awt.Rectangle; +import java.io.File; +import java.io.IOException; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Locale; +import java.util.Map; + +import javax.swing.JInternalFrame; + +import org.testng.Assert; +import org.testng.AssertJUnit; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + import jalview.analysis.scoremodels.SimilarityParams; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureColourI; import jalview.api.ViewStyleI; +import jalview.bin.Cache; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +import jalview.datamodel.ContactListI; +import jalview.datamodel.ContactMatrix; +import jalview.datamodel.ContactMatrixI; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.GeneLocus; import jalview.datamodel.HiddenSequences; +import jalview.datamodel.Mapping; import jalview.datamodel.PDBEntry; import jalview.datamodel.PDBEntry.Type; +import jalview.datamodel.Sequence.DBModList; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; @@ -49,8 +76,10 @@ import jalview.gui.AlignViewport; import jalview.gui.AlignmentPanel; import jalview.gui.Desktop; import jalview.gui.JvOptionPane; +import jalview.gui.OverviewPanel; import jalview.gui.PCAPanel; import jalview.gui.PopupMenu; +import jalview.gui.Preferences; import jalview.gui.SliderPanel; import jalview.io.DataSourceType; import jalview.io.FileFormat; @@ -67,24 +96,11 @@ import jalview.schemes.RNAHelicesColour; import jalview.schemes.StrandColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.structure.StructureImportSettings; +import jalview.util.MapList; import jalview.util.matcher.Condition; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.seqfeatures.FeatureRendererModel; - -import java.awt.Color; -import java.io.File; -import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import javax.swing.JInternalFrame; - -import org.testng.Assert; -import org.testng.AssertJUnit; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; @Test(singleThreaded = true) public class Jalview2xmlTests extends Jalview2xmlBase @@ -94,6 +110,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase @BeforeClass(alwaysRun = true) public void setUpJvOptionPane() { + if (Desktop.instance != null) + Desktop.instance.closeAll_actionPerformed(null); JvOptionPane.setInteractiveMode(false); JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } @@ -109,65 +127,74 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertNotNull(af, "Didn't read input file " + inFile); int olddsann = countDsAnn(af.getViewport()); assertTrue(olddsann > 0, "Didn't find any dataset annotations"); - af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices - .toString()); + af.changeColour_actionPerformed( + JalviewColourScheme.RNAHelices.toString()); assertTrue( - af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour, + af.getViewport() + .getGlobalColourScheme() instanceof RNAHelicesColour, "Couldn't apply RNA helices colourscheme"); - assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), + af.saveAlignment(tfile, FileFormat.Jalview); + assertTrue(af.isSaveAlignmentSuccessful(), "Failed to store as a project."); af.closeMenuItem_actionPerformed(true); af = null; - af = new FileLoader() - .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE); + af = new FileLoader().LoadFileWaitTillLoaded(tfile, + DataSourceType.FILE); assertNotNull(af, "Failed to import new project"); int newdsann = countDsAnn(af.getViewport()); assertEquals(olddsann, newdsann, "Differing numbers of dataset sequence annotation\nOriginally " + olddsann + " and now " + newdsann); - System.out - .println("Read in same number of annotations as originally present (" + System.out.println( + "Read in same number of annotations as originally present (" + olddsann + ")"); assertTrue( - af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour, + af.getViewport() + .getGlobalColourScheme() instanceof RNAHelicesColour, "RNA helices colourscheme was not applied on import."); } @Test(groups = { "Functional" }) public void testTCoffeeScores() throws Exception { - String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii"; + String inFile = "examples/uniref50.fa", + inAnnot = "examples/uniref50.score_ascii"; String tfile = File.createTempFile("JalviewTest", ".jvp") .getAbsolutePath(); AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, DataSourceType.FILE); assertNotNull(af, "Didn't read input file " + inFile); af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null); - assertSame(af.getViewport().getGlobalColourScheme().getClass(), + AlignViewport viewport = af.getViewport(); + assertSame(viewport.getGlobalColourScheme().getClass(), TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme"); - assertNotNull(ColourSchemeProperty.getColourScheme(af.getViewport() - .getAlignment(), af.getViewport().getGlobalColourScheme() - .getSchemeName()), "Recognise T-Coffee score from string"); - - assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), + assertNotNull( + ColourSchemeProperty.getColourScheme(viewport, + viewport.getAlignment(), + viewport.getGlobalColourScheme().getSchemeName()), + "Recognise T-Coffee score from string"); + + af.saveAlignment(tfile, FileFormat.Jalview); + assertTrue(af.isSaveAlignmentSuccessful(), "Failed to store as a project."); af.closeMenuItem_actionPerformed(true); af = null; - af = new FileLoader() - .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE); + af = new FileLoader().LoadFileWaitTillLoaded(tfile, + DataSourceType.FILE); assertNotNull(af, "Failed to import new project"); assertSame(af.getViewport().getGlobalColourScheme().getClass(), TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme for imported project."); - System.out - .println("T-Coffee score shading successfully recovered from project."); + System.out.println( + "T-Coffee score shading successfully recovered from project."); } @Test(groups = { "Functional" }) public void testColourByAnnotScores() throws Exception { - String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva"; + String inFile = "examples/uniref50.fa", + inAnnot = "examples/testdata/uniref50_iupred.jva"; String tfile = File.createTempFile("JalviewTest", ".jvp") .getAbsolutePath(); AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, @@ -178,12 +205,12 @@ public class Jalview2xmlTests extends Jalview2xmlBase .getSequenceAt(0).getAnnotation("IUPredWS (Short)"); assertTrue( - aa != null && aa.length > 0, + aa != null && aa.length > 0, "Didn't find any IUPred annotation to use to shade alignment."); AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null, AnnotationColourGradient.ABOVE_THRESHOLD); - AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0], - null, AnnotationColourGradient.BELOW_THRESHOLD); + AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0], null, + AnnotationColourGradient.BELOW_THRESHOLD); cs.setSeqAssociated(true); gcs.setSeqAssociated(true); af.changeColour(cs); @@ -195,19 +222,20 @@ public class Jalview2xmlTests extends Jalview2xmlBase sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false); sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true); af.alignPanel.alignmentChanged(); - assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), + af.saveAlignment(tfile, FileFormat.Jalview); + assertTrue(af.isSaveAlignmentSuccessful(), "Failed to store as a project."); af.closeMenuItem_actionPerformed(true); af = null; - af = new FileLoader() - .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE); + af = new FileLoader().LoadFileWaitTillLoaded(tfile, + DataSourceType.FILE); assertNotNull(af, "Failed to import new project"); // check for group and alignment colourschemes ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme(); - ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups() - .get(0).getColourScheme(); + ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups().get(0) + .getColourScheme(); assertNotNull(_rcs, "Didn't recover global colourscheme"); assertTrue(_rcs instanceof AnnotationColourGradient, "Didn't recover annotation colour global scheme"); @@ -217,8 +245,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase boolean diffseqcols = false, diffgseqcols = false; SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray(); - for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize - && (!diffseqcols || !diffgseqcols); p++) + for (int p = 0, pSize = af.getViewport().getAlignment() + .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) { if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f)) @@ -227,8 +255,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase } } assertTrue(diffseqcols, "Got Different sequence colours"); - System.out - .println("Per sequence colourscheme (Background) successfully applied and recovered."); + System.out.println( + "Per sequence colourscheme (Background) successfully applied and recovered."); assertNotNull(_rgcs, "Didn't recover group colourscheme"); assertTrue(_rgcs instanceof AnnotationColourGradient, @@ -237,25 +265,26 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertTrue(__rcs.isSeqAssociated(), "Group Annotation colourscheme wasn't sequence associated"); - for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize - && (!diffseqcols || !diffgseqcols); p++) + for (int p = 0, pSize = af.getViewport().getAlignment() + .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) { - if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs - .findColour(sqs[2].getCharAt(p), p, sqs[2], null, 0f)) + if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, + 0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null, + 0f)) { diffgseqcols = true; } } assertTrue(diffgseqcols, "Got Different group sequence colours"); - System.out - .println("Per sequence (Group) colourscheme successfully applied and recovered."); + System.out.println( + "Per sequence (Group) colourscheme successfully applied and recovered."); } @Test(groups = { "Functional" }) public void gatherViewsHere() throws Exception { - int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop - .getAlignFrames().length; + int origCount = Desktop.getAlignFrames() == null ? 0 + : Desktop.getAlignFrames().length; AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/exampleFile_2_7.jar", DataSourceType.FILE); assertNotNull(af, "Didn't read in the example file correctly."); @@ -336,14 +365,14 @@ public class Jalview2xmlTests extends Jalview2xmlBase sq.findPosition(p); try { - assertTrue( - (alaa.annotations[p] == null && refan.annotations[p] == null) - || alaa.annotations[p].value == refan.annotations[p].value, + assertTrue((alaa.annotations[p] == null + && refan.annotations[p] == null) + || alaa.annotations[p].value == refan.annotations[p].value, "Mismatch at alignment position " + p); } catch (NullPointerException q) { - Assert.fail("Mismatch of alignment annotations at position " - + p + " Ref seq ann: " + refan.annotations[p] + Assert.fail("Mismatch of alignment annotations at position " + p + + " Ref seq ann: " + refan.annotations[p] + " alignment " + alaa.annotations[p]); } } @@ -378,10 +407,10 @@ public class Jalview2xmlTests extends Jalview2xmlBase AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle)); groups.getAlignViewport().setViewStyle(structureStyle); - AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport() - .getViewStyle())); - Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport() - .getViewStyle())); + AssertJUnit.assertFalse( + groupStyle.sameStyle(groups.getAlignViewport().getViewStyle())); + Assert.assertTrue(structureStyle + .sameStyle(groups.getAlignViewport().getViewStyle())); } @@ -402,9 +431,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase // check FileLoader returned a reference to the one alignFrame that is // actually on the Desktop - assertSame( - af, - Desktop.getAlignFrameFor(af.getViewport()), + assertSame(af, Desktop.getAlignFrameFor(af.getViewport()), "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window"); Desktop.explodeViews(af); @@ -431,11 +458,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), DataSourceType.FILE); Assert.assertNotNull(af); - Assert.assertEquals( - Desktop.getAlignFrames().length, - Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length); - Assert.assertEquals( - Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length, + Assert.assertEquals(Desktop.getAlignFrames().length, + Desktop.getAlignmentPanels( + af.getViewport().getSequenceSetId()).length); + Assert.assertEquals(Desktop + .getAlignmentPanels(af.getViewport().getSequenceSetId()).length, oldviews); } @@ -537,8 +564,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test")); assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST")); assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test")); - assertTrue(Jalview2XML - .isVersionStringLaterThan(null, "Automated Build")); + assertTrue( + Jalview2XML.isVersionStringLaterThan(null, "Automated Build")); assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Automated Build")); assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", @@ -570,6 +597,16 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3")); assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1")); assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1")); + /* + * test for patch release versions + */ + assertFalse(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.2")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.4")); + assertFalse( + Jalview2XML.isVersionStringLaterThan("2.12.2.0b1", "2.12.2.0")); + assertFalse( + Jalview2XML.isVersionStringLaterThan("2.12.2.3", "2.12.2.2")); + } /** @@ -647,8 +684,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase n++; } - File tfile = File - .createTempFile("testStoreAndRecoverGroupReps", ".jvp"); + File tfile = File.createTempFile("testStoreAndRecoverGroupReps", + ".jvp"); try { new Jalview2XML(false).saveState(tfile); @@ -687,9 +724,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase */ List hidden = hiddenSeqNames.get(ap.getViewName()); HiddenSequences hs = alignment.getHiddenSequences(); - assertEquals( - hidden.size(), - hs.getSize(), + assertEquals(hidden.size(), hs.getSize(), "wrong number of restored hidden sequences in " + ap.getViewName()); } @@ -731,14 +766,18 @@ public class Jalview2xmlTests extends Jalview2xmlBase pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile); pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile); pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile); - Assert.assertEquals(seqs[0].getDatasetSequence().getAllPDBEntries() - .get(0), pdbEntries[0]); - Assert.assertEquals(seqs[1].getDatasetSequence().getAllPDBEntries() - .get(0), pdbEntries[1]); - Assert.assertEquals(seqs[2].getDatasetSequence().getAllPDBEntries() - .get(0), pdbEntries[2]); - Assert.assertEquals(seqs[3].getDatasetSequence().getAllPDBEntries() - .get(0), pdbEntries[3]); + Assert.assertEquals( + seqs[0].getDatasetSequence().getAllPDBEntries().get(0), + pdbEntries[0]); + Assert.assertEquals( + seqs[1].getDatasetSequence().getAllPDBEntries().get(0), + pdbEntries[1]); + Assert.assertEquals( + seqs[2].getDatasetSequence().getAllPDBEntries().get(0), + pdbEntries[2]); + Assert.assertEquals( + seqs[3].getDatasetSequence().getAllPDBEntries().get(0), + pdbEntries[3]); File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp"); try @@ -786,6 +825,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase "Mismatch PDBEntry 'Type'"); Assert.assertNotNull(recov.getFile(), "Recovered PDBEntry should have a non-null file entry"); + Assert.assertEquals( + recov.getFile().toLowerCase(Locale.ENGLISH) + .lastIndexOf("pdb"), + recov.getFile().length() - 3, + "Recovered PDBEntry file should have PDB suffix"); } } @@ -797,6 +841,95 @@ public class Jalview2xmlTests extends Jalview2xmlBase * @throws IOException */ @Test(groups = { "Functional" }) + public void testStoreAndRecoverAnnotationRowElementColours() + throws IOException + { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded("SEQ\tMNQ", + DataSourceType.PASTE); + + AlignViewport av = af.getViewport(); + AlignmentI al = av.getAlignment(); + SequenceI fsq; + fsq = al.getSequenceAt(0); + Annotation annots[] = new Annotation[fsq.getLength()]; + AlignmentAnnotation ala = new AlignmentAnnotation("Colour", "Annots", + annots); + annots[0] = new Annotation(1.0f); + annots[1] = new Annotation(2.0f); + annots[2] = new Annotation(3.0f); + annots[0].colour = Color.RED; + annots[1].colour = Color.GREEN; + annots[2].colour = Color.BLUE; + ala.validateRangeAndDisplay(); + al.getSequenceAt(0).addAlignmentAnnotation(ala); + al.addAnnotation(ala); + /* + * and colour by annotation + */ + AnnotationColourGradient acg = new AnnotationColourGradient(ala, + af.alignPanel.av.getGlobalColourScheme(), 0); + acg.setSeqAssociated(true); + acg.setPredefinedColours(true); + af.changeColour(acg); + Color seqcol[] = new Color[3]; + for (int iStart = fsq.findIndex(fsq.getStart()), i = 0; i < 3; i++) + { + seqcol[i] = af.alignPanel.getSeqPanel().seqCanvas + .getSequenceRenderer() + .getResidueColour(fsq, iStart + i, null); + } + /* + * save project, close windows, reload project, verify + */ + File tfile = File.createTempFile( + "testStoreAndRecoverAnnotRowElemColors", ".jvp"); + tfile.deleteOnExit(); + new Jalview2XML(false).saveState(tfile); + // Desktop.instance.closeAll_actionPerformed(null); + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + Assert.assertNotNull(af, "Failed to reload project"); + /* + * verify alignment annotation has colors + */ + av = af.getViewport(); + + ColourSchemeI loadedCscheme = av.getGlobalColourScheme(); + Assert.assertTrue(loadedCscheme instanceof AnnotationColourGradient, + "Didn't apply Annotation colour gradient"); + acg = (AnnotationColourGradient) loadedCscheme; + assertTrue(acg.isSeqAssociated()); + assertTrue(acg.isPredefinedColours()); + + al = av.getAlignment(); + fsq = al.getSequenceAt(0); + ala = fsq.getAnnotation()[0]; + Assert.assertNotNull(ala, "No annotation row recovered"); + Assert.assertNotNull(ala.annotations); + for (int iStart = al.getSequenceAt(0) + .findIndex(al.getSequenceAt(0).getStart()), i = 0; i < 3; i++) + { + Assert.assertTrue(ala.annotations[i].colour != null); + Assert.assertTrue(ala.annotations[i].colour.equals(annots[i].colour)); + Color newseqcol = af.alignPanel.getSeqPanel().seqCanvas + .getSequenceRenderer() + .getResidueColour(fsq, iStart + i, null); + Assert.assertTrue(seqcol[i].equals(newseqcol), + "Sequence shading is different"); + + } + + } + + /** + * Configure an alignment and a sub-group each with distinct colour schemes, + * Conservation and PID thresholds, and confirm these are restored from the + * saved project. + * + * @throws IOException + */ + @Test(groups = { "Functional" }) public void testStoreAndRecoverColourThresholds() throws IOException { Desktop.instance.closeAll_actionPerformed(null); @@ -809,6 +942,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase /* * Colour alignment by Buried Index, Above 10% PID, By Conservation 20% */ + av.setColourAppliesToAllGroups(false); af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString()); assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme); af.abovePIDThreshold_actionPerformed(true); @@ -827,15 +961,18 @@ public class Jalview2xmlTests extends Jalview2xmlBase /* * create a group with Strand colouring, 30% Conservation * and 40% PID threshold + * (notice menu action applies to selection group even if mouse click + * is at a sequence not in the group) */ SequenceGroup sg = new SequenceGroup(); sg.addSequence(al.getSequenceAt(0), false); sg.setStartRes(15); sg.setEndRes(25); av.setSelectionGroup(sg); - PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null); - popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand - .toString()); + PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2), + null); + popupMenu.changeColour_actionPerformed( + JalviewColourScheme.Strand.toString()); assertTrue(sg.getColourScheme() instanceof StrandColourScheme); assertEquals(al.getGroups().size(), 1); assertSame(al.getGroups().get(0), sg); @@ -921,8 +1058,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase fr.setColour("type2", byLabel); // type3: by score above threshold - FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1, - 10); + FeatureColourI byScore = new FeatureColour(null, Color.BLACK, + Color.BLUE, null, 1, 10); byScore.setAboveThreshold(true); byScore.setThreshold(2f); fr.setColour("type3", byScore); @@ -934,8 +1071,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase fr.setColour("type4", byAF); // type5: by attribute CSQ:PolyPhen below threshold - FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE, - 1, 10); + FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK, + Color.BLUE, null, 1, 10); byPolyPhen.setBelowThreshold(true); byPolyPhen.setThreshold(3f); byPolyPhen.setAttributeName("CSQ", "PolyPhen"); @@ -970,7 +1107,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase File tfile = File.createTempFile("JalviewTest", ".jvp"); tfile.deleteOnExit(); String filePath = tfile.getAbsolutePath(); - assertTrue(af.saveAlignment(filePath, FileFormat.Jalview), + af.saveAlignment(filePath, FileFormat.Jalview); + assertTrue(af.isSaveAlignmentSuccessful(), "Failed to store as a project."); /* @@ -978,8 +1116,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase */ af.closeMenuItem_actionPerformed(true); af = null; - af = new FileLoader() - .LoadFileWaitTillLoaded(filePath, DataSourceType.FILE); + af = new FileLoader().LoadFileWaitTillLoaded(filePath, + DataSourceType.FILE); assertNotNull(af, "Failed to import new project"); /* @@ -1012,7 +1150,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertEquals(fr.getFeatureFilter("type2").toStableString(), "(Score LE 2.4) AND (Score GT 1.1)"); assertEquals(fr.getFeatureFilter("type3").toStableString(), - "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)"); + "(AF Contains X) OR (CSQ:PolyPhen NE 0)"); } private void addFeature(SequenceI seq, String featureType, int score) @@ -1168,4 +1306,306 @@ public class Jalview2xmlTests extends Jalview2xmlBase .getAlignViewport(), "Didn't restore correct view association for the PCA view"); } + + /** + * Test save and reload of DBRefEntry including GeneLocus in project + * + * @throws Exception + */ + @Test(groups = { "Functional" }) + public void testStoreAndRecoverGeneLocus() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + String seqData = ">P30419\nACDE\n>X1235\nGCCTGTGACGAA"; + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData, + DataSourceType.PASTE); + assertNotNull(af, "Didn't read in the example file correctly."); + + AlignmentViewPanel ap = Desktop.getAlignmentPanels(null)[0]; + SequenceI pep = ap.getAlignment().getSequenceAt(0); + SequenceI cds = ap.getAlignment().getSequenceAt(1); + + /* + * give 'protein' a dbref to self, a dbref with map to CDS, + * and a dbref with map to gene 'locus' + */ + DBRefEntry dbref1 = new DBRefEntry("Uniprot", "1", "P30419", null); + pep.addDBRef(dbref1); + Mapping cdsmap = new Mapping(cds, + new MapList(new int[] + { 1, 4 }, new int[] { 1, 12 }, 1, 3)); + DBRefEntry dbref2 = new DBRefEntry("EMBLCDS", "2", "X1235", cdsmap); + pep.addDBRef(dbref2); + Mapping locusmap = new Mapping(null, + new MapList(new int[] + { 1, 4 }, new int[] { 2674123, 2674135 }, 1, 3)); + DBRefEntry dbref3 = new GeneLocus("human", "GRCh38", "5", locusmap); + pep.addDBRef(dbref3); + + File tfile = File.createTempFile("testStoreAndRecoverGeneLocus", + ".jvp"); + try + { + new Jalview2XML(false).saveState(tfile); + } catch (Throwable e) + { + Assert.fail("Didn't save the state", e); + } + Desktop.instance.closeAll_actionPerformed(null); + + new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0]; + SequenceI rpep = rap.getAlignment().getSequenceAt(0); + DBModList dbrefs = rpep.getDBRefs(); + assertEquals(rpep.getName(), "P30419"); + assertEquals(dbrefs.size(), 3); + DBRefEntry dbRef = dbrefs.get(0); + assertFalse(dbRef instanceof GeneLocus); + assertNull(dbRef.getMap()); + assertEquals(dbRef, dbref1); + + /* + * restored dbrefs with mapping have a different 'map to' + * sequence but otherwise match the original dbrefs + */ + dbRef = dbrefs.get(1); + assertFalse(dbRef instanceof GeneLocus); + assertTrue(dbRef.equalRef(dbref2)); + assertNotNull(dbRef.getMap()); + SequenceI rcds = rap.getAlignment().getSequenceAt(1); + assertSame(dbRef.getMap().getTo(), rcds); + // compare MapList but not map.to + assertEquals(dbRef.getMap().getMap(), dbref2.getMap().getMap()); + + /* + * GeneLocus map.to is null so can compare Mapping objects + */ + dbRef = dbrefs.get(2); + assertTrue(dbRef instanceof GeneLocus); + assertEquals(dbRef, dbref3); + } + + /** + * test store and recovery of Overview windows + * + * @throws Exception + */ + @Test(groups = { "Functional" }, enabled = true) + public void testStoreAndRecoverOverview() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + + Cache.setProperty("SHOW_OVERVIEW", "false"); + Cache.setProperty(Preferences.USE_LEGACY_GAP, "false"); + Cache.setColourProperty(Preferences.GAP_COLOUR, Color.green); + Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.yellow); + Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "true"); + + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + + /* + * open and resize / reposition overview + */ + af.overviewMenuItem_actionPerformed(null); + OverviewPanel ov1 = af.alignPanel.getOverviewPanel(); + assertNotNull(ov1); + ov1.setFrameBounds(20, 30, 200, 400); + assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa"); + assertTrue(ov1.isShowHiddenRegions()); + + /* + * open a New View and its Overview and reposition it + */ + af.newView_actionPerformed(null); + af.overviewMenuItem_actionPerformed(null); + OverviewPanel ov2 = af.alignPanel.getOverviewPanel(); + assertNotNull(ov2); + assertNotSame(ov1, ov2); + ov2.setFrameBounds(25, 35, 205, 405); + assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original"); + assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1"); + + File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp"); + new Jalview2XML(false).saveState(tfile); + Desktop.instance.closeAll_actionPerformed(null); + + /* + * change preferences (should _not_ affect reloaded Overviews) + */ + Cache.setProperty("SHOW_OVERVIEW", "true"); + Cache.setProperty(Preferences.USE_LEGACY_GAP, "true"); + Cache.setColourProperty(Preferences.GAP_COLOUR, Color.blue); + Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.orange); + Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "false"); + + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + + /* + * workaround: explicitly select View 1 (not in focus after restore) + */ + af.tabSelectionChanged(1); + + /* + * verify restored overview for View 1 + */ + ov2 = af.alignPanel.getOverviewPanel(); + assertEquals(ov2.getCanvas().getGapColour(), Color.green); + // 'non-legacy' colouring uses white for non-gapped residues + assertEquals(ov2.getCanvas().getResidueColour(), Color.white); + assertEquals(ov2.getCanvas().getHiddenColour(), Color.yellow); + assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1"); + assertEquals(ov2.getFrameBounds(), new Rectangle(25, 35, 205, 405)); + assertTrue(ov2.isShowHiddenRegions()); + + /* + * verify restored overview for Original view + */ + af.tabSelectionChanged(0); + ov1 = af.alignPanel.getOverviewPanel(); + assertEquals(ov1.getCanvas().getGapColour(), Color.green); + // 'non-legacy' colouring uses white for non-gapped residues + assertEquals(ov1.getCanvas().getResidueColour(), Color.white); + assertEquals(ov1.getCanvas().getHiddenColour(), Color.yellow); + assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original"); + assertEquals(ov1.getFrameBounds(), new Rectangle(20, 30, 200, 400)); + assertTrue(ov1.isShowHiddenRegions()); + } + + /** + * Test that a view with no Overview is restored with no Overview, even if + * 'Open Overview' is selected in Preferences + * + * @throws Exception + */ + @Test(groups = { "Functional" }, enabled = true) + public void testStoreAndRecoverNoOverview() throws Exception + { + Cache.setProperty("SHOW_OVERVIEW", "false"); + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE); + + File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp"); + new Jalview2XML(false).saveState(tfile); + Desktop.instance.closeAll_actionPerformed(null); + + Cache.setProperty("SHOW_OVERVIEW", "true"); + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + + assertNull(af.alignPanel.getOverviewPanel()); + } + + /** + * Test that a view from an older version of Jalview is restored with Overview + * automatically shown when the preference is set + * + * @throws Exception + */ + @Test(groups = { "Functional" }, enabled = true) + public void testAutoShowOverviewForLegacyProjects() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + Cache.setProperty("SHOW_OVERVIEW", "true"); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile.jvp", DataSourceType.FILE); + + Cache.setProperty("SHOW_OVERVIEW", "false"); + assertNotNull(af.alignPanel.getOverviewPanel()); + } + + /** + * Test that loading example.jvp, doing some stuff, then hitting reload + * doesn't leave the modified window still open + * + * See JAL-4127 - interactively performing the same actions and reloading + * works fine, but programmatically they do not + * + * @throws Exception + */ + @Test(groups = { "Functional" }, enabled = false) + public void testReloadActuallyReloads() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile.jvp", DataSourceType.FILE); + af.getViewport().getColumnSelection().addElement(3); + af.hideSelColumns_actionPerformed(null); + af.newView("new", true); + af.reload_actionPerformed(null); + Thread.sleep(30); + // af exists still but isn't shown + assertTrue(af.isClosed()); + } + + @Test(groups = { "Functional" }) + public void testPAEsaveRestore() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE); + AlignmentI al = af.getViewport().getAlignment(); + // PAE matrices are added as reference annotation to the dataset sequence + // at least for now. + SequenceI sq = al.getSequenceAt(0).getDatasetSequence(); + int i = sq.getLength(); + float[][] paevals = new float[i][i]; + for (i = i - 1; i >= 0; i--) + { + for (int j = 0; j <= i; j++) + { + paevals[i][j] = ((i - j < 2) + || ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f; + paevals[j][i] = paevals[i][j]; + } + } + PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals); + String content = ContactMatrix.contactToFloatString(dummyMat); + Assert.assertTrue(content.contains("\t1.")); // at least one element must be + // 1 + float[][] vals = ContactMatrix.fromFloatStringToContacts(content, + sq.getLength(), sq.getLength()); + assertEquals(vals[3][4], paevals[3][4]); + dummyMat.makeGroups(0.5f, false); + Assert.assertNotSame(dummyMat.getNewick(), ""); + AlignmentAnnotation paeCm = sq.addContactList(dummyMat); + al.addAnnotation(paeCm); + File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix", + ".jvp"); + new Jalview2XML(false).saveState(tfile); + Desktop.instance.closeAll_actionPerformed(null); + + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + AlignmentI newAl = af.getViewport().getAlignment(); + SequenceI newSeq = newAl.getSequenceAt(0).getDatasetSequence(); + // check annotation of the expected type exists + Assert.assertEquals(newSeq.getAnnotation().length, 1); + Assert.assertEquals(newSeq.getAnnotation()[0].graph, paeCm.graph); + + // check a contact matrix was recovered + Assert.assertEquals(newSeq.getContactMaps().size(), 1); + // and can be found for the annotation on the sequence + ContactMatrixI restoredMat = newSeq + .getContactMatrixFor(newSeq.getAnnotation()[0]); + Assert.assertNotNull(restoredMat); + for (i = sq.getLength() - 1; i >= 0; i--) + { + ContactListI oldCM = dummyMat.getContactList(i), + newCM = restoredMat.getContactList(i); + for (int j = oldCM.getContactHeight(); j >= 0; j--) + { + Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j)); + } + } + Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups()); + Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups()); + Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree()); + Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick()); + + } + }